Add the DeepDDS model
See original GitHub issue- Please read the paper first. It is here.
- There is also code-release with the paper here.
- After that read the contributing guidelines.
- If there is an existing open-source version of the model please take a look.
- ChemicalX is built on top of PyTorch 1.10. and torchdrug.
- The library heavily builds on top on torchdrug and molecules in batches are PackedGraphs.
- There is already a model class under
./chemicalx/models/
- Context features, drug level features, and labels are all FloatTensors.
- Look at the examples and tests under
./examples/
and./tests/
. - Add auxiliary layers as you see fit - please document these, add tests, and add these layers to the main readme.md if needed.
- Add typing to the initialization and forward pass.
- Non-data-dependent hyper-ammeters should have default values.
- Please add tests under
./tests/
and make sure that your model/layer is tested with real data. - Write an example under
./examples/
. What is the AUC on the test set? Is it reasonable?
Issue Analytics
- State:
- Created 2 years ago
- Reactions:1
- Comments:6 (4 by maintainers)
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DeepDDS: deep graph neural network with attention ... - arXiv
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Read more >DeepDDS: deep graph neural network with attention ... - bioRxiv
Results In this paper, we proposed a deep learning model based on graph neural networks and attention mechanism to identify drug combinations ...
Read more >(PDF) DeepDDS: deep graph neural network with attention ...
In this paper, we proposed a deep learning model based on graph neural networks and attention mechanism to identify drug combinations that ...
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Read more >DeepDDS — chemicalx documentation - Read the Docs
Bases: chemicalx.models.base.Model. An implementation of the DeepDDS model from [wang2021]. This implementation follows the code on github where the paper ...
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Okay, let me switch around in a moment.
I think it would be better to give Klas the easier one 😃